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polyGBLUP: a modified genomic best linear unbiased prediction improved the genomic prediction efficiency for autopolyploid species

文献类型： 外文期刊

作者： Song, Hailiang 1 ; Zhang, Qin 4 ; Hu, Hongxia 1 ;

作者机构： 1.Beijing Acad Agr & Forestry Sci, Fisheries Sci Inst, Beijing 100068, Peoples R China

2.Beijing Key Lab Fisheries Biotechnol, Beijing 100068, Peoples R China

3.Minist Agr & Rural Affairs, Key Lab Sturgeon Genet & Breeding, Hangzhou 311799, Peoples R China

4.Shandong Agr Univ, Shandong Prov Key Lab Anim Biotechnol & Dis Contro, Tai An 271001, Peoples R China

关键词： autopolyploid species; genomic prediction; genomic best linear unbiased prediction; allele dosages; dominance effects

期刊名称：BRIEFINGS IN BIOINFORMATICS （ 影响因子：6.8； 五年影响因子：7.9 ）

ISSN： 1467-5463

年卷期： 2024 年 25 卷 2 期

页码：

收录情况： SCI

摘要： Given the universality of autopolyploid species in nature, it is crucial to develop genomic selection methods that consider different allele dosages for autopolyploid breeding. However, no method has been developed to deal with autopolyploid data regardless of the ploidy level. In this study, we developed a modified genomic best linear unbiased prediction (GBLUP) model (polyGBLUP) through constructing additive and dominant genomic relationship matrices based on different allele dosages. polyGBLUP could carry out genomic prediction for autopolyploid species regardless of the ploidy level. Through comprehensive simulations and analysis of real data of autotetraploid blueberry and guinea grass and autohexaploid sweet potato, the results showed that polyGBLUP achieved higher prediction accuracy than GBLUP and its superiority was more obvious when the ploidy level of autopolyploids is high. Furthermore, when the dominant effect was added to polyGBLUP (polyGDBLUP), the greater the dominance degree, the more obvious the advantages of polyGDBLUP over the diploid models in terms of prediction accuracy, bias, mean squared error and mean absolute error. For real data, the superiority of polyGBLUP over GBLUP appeared in blueberry and sweet potato populations and a part of the traits in guinea grass population due to the high correlation coefficients between diploid and polyploidy genomic relationship matrices. In addition, polyGDBLUP did not produce higher prediction accuracy than polyGBLUP for most traits of real data as dominant genetic variance was not captured for these traits. Our study will be a significant promising method for genomic prediction of autopolyploid species.

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